Being an MKIV VR6 owner (Jetta) myself, and one with 100k miles and no problems (other than a constant Check Engine Light, you'll learn to love it); I say GO FOR IT!

The few problems that these cars do have (which I have had none of) -- like coilpacks and door regulators and such, are all covered by service bulletins at the dealership free of charge.

VW has, in my experience, taken very good care of issues with their vehicles.

Like I said, I've had none with mine.